Location: Wheat Health, Genetics, and Quality Research
2017 Annual Report
Objectives
The long-term objective of this project is to develop biologically based technologies for controlling soilborne pathogens of wheat, barley and brassica crops grown as part of cereal-based production systems. Three specific objectives will be addressed over the next five years.
Objective 1: Define the pathogen diversity, host range, and geographical distribution of fungal and nematode root pathogens, especially those causing emerging diseases in cereal-based cropping systems in the Pacific Northwest.
Subobjective 1A: Using conventional and molecular techniques, determine the biogeographical distribution and risk of emerging and chronic pathogens and diseases.
Subobjective 1B: Examine the genetic and pathogenic diversity of emerging and chronic pathogens.
Subobjective 1C: Develop and evaluate agronomic, genetic and cultural methods of root disease management.
Objective 2: Determine the soil microorganisms, microbial communities, and molecular mechanisms that promote or reduce plant health in wheat, barley and canola in the Pacific Northwest.
Subobjective 2A: Determine how cultural practices and chemical inputs affect the plant and soil microbiomes in wheat cropping systems.
Subobjective 2B: Characterize the rhizosphere microbiome of wheat in take-all decline soils.
Subobjective 2C: Evaluate the effect of the wheat cultivar on the robustness of biological control by Pseudomonas spp. and in take-all decline soils.
Objective 3: Identify and characterize molecular mechanisms of host-microbe interactions, including the action of host genes governing disease resistance and biological control against soilborne pathogens of wheat, barley and canola.
Subobjective 3A: Identify host responses to soilborne pathogens, biocontrol bacteria and bacterial metabolites.
Subobjective 3B: Identify and characterize germplasm with resistance to soilborne pathogens.
Approach
Biological control of soilborne fungal pathogens such as Gaeumannomyces, Rhizoctonia, Pythium, Fusarium and plant-parasitic nematodes by naturally-occurring and recombinant microorganisms will be developed and quantified in agricultural soils. Molecular approaches will be used to detect and quantify soilborne pathogens and their microbial antagonists, and next-generation sequencing will be used to characterize the microbiomes of conducive and suppressive soils and the rhizosphere of small grain crops. Genetic determinants and molecular mechanisms responsible for root colonization and pathogen suppression will be characterized with emphasis on the genetics and regulation of phenazine and phloroglucinol biosynthesis in vitro and in situ. The genetic and physiological diversity of populations of root pathogens and their microbial antagonists, and influence of cropping systems on pathogens and antagonists will be determined. Genomes of pathogens and antagonists will be sequenced and analyzed. New sources and mechanisms of host resistance will be identified. Practical disease control will be accomplished by maximizing the activity of natural biocontrol agents.
Progress Report
This is the first report for this new project which began in March of 2017. Please see the report for the previous project, 2090-22000-016-00D, "Biology and Biological Control of Root Diseases of Wheat, Barley and Biofuel Brassicas”, for additional information. Wheat, barley and biofuel crops are infected by soilborne pathogens that reduce yields ten to thirty percent annually. Diseased crops cannot take full advantage of fertilizers and irrigation water, and unused nitrates move into surface and ground water and pollute the environment. The overarching goal of this project is to develop biologically-based technology for controlling root diseases of wheat, barley and biofuel brassica crops; to identify the diversity, host range, and geographical distribution of root pathogens, especially those causing emerging diseases; to determine the soil microbes, microbial communities, and molecular mechanisms that promote or reduce plant health, and to characterize the host-microbe interactions involved in disease resistance and biocontrol of root diseases. Progress was made on all three objectives and their subobjectives, all of which fall under NP 303 and encompass Component 1 Problem 1A, Component 2 Problem 2C or Component 3 Problem 3A or B.
Under Objective 1.A, we continued to monitor for existing and emerging diseases in Washington. This includes cereal cyst nematode (Heterodera avenae and H. avenae) and black leg of canola (Leptosphaeria maculans) and involves making collections, extracting and sequencing DNA, and making identifications. We have also started to make collections of Fusarium graminearum, the cause of head blight. This is becoming an increasing problem in irrigated wheat, especially in rotation with corn.
Under Objective 2.B, working with collaborators at Washington State University and the Pacific Northwest National Laboratory, we used highly advanced imaging techniques on wheat roots and showed that the natural antibiotic phenazine-1-carboxylic acid (PCA), produced by pseudomonas bacteria, promotes both biofilm development and turnover of rhizobacterial biomass in a soil moisture-dependent manner. PCA produced in the rhizosphere profoundly influence plant health and development, but its impact on soil nutrient dynamics and organic matter previously was poorly understood due to spatial and biochemical heterogeneity. These results are important because they show that a single key group of bacteria, PCA producing-pseudomonads, within the milieu of the wheat microbiome significantly impacts soil health, function and structure.
Under Objective 3.B, we made significant progress in developing genetic resistance to Rhizoctonia root rot and bare patch, the most important disease of direct-seeded wheat and barley in the Pacific Northwest. All Northwest cultivars of wheat and barley are susceptible to this disease, which causes 10-30% annual yield losses. Working with Washington State University colleagues, we found that resistance is conferred by multiple genes in two of the five most promising synthetic wheats. The multi-gene resistance can be transferred to adapted wheat cultivars. In addition, by comparing resistant and susceptible wheat plants representing three distinct types of resistance, we demonstrated that resistance to Rhizoctonia root rot is negatively correlated to early root growth. This new discovery will enable rapid identification of candidate resistant plants, and will shorten the screening interval up to five-fold.
Accomplishments
1. Blackleg identified in Washington State and becoming more widespread. Blackleg of canola is the most serious disease of crucifers worldwide. Until a few years ago, the Pacific Northwest was considered free of this disease, but in 2014 it was discovered in the Willamette Valley of Oregon and in the Camus Prairie of Idaho in Spring of 2015. ARS scientists in Pullman, Washington, in collaboration with state and county colleagues, launched surveys, grower talks, extension publications and other information to warn growers in Washington about this seed-borne disease, and how to keep from getting it in Washington. Because of very favorable conditions in 2016-2017, we documented a number of finds throughout Washington State. However, these outbreaks have been contained as the industry was proactively mobilized. The data needed by the Washington State Department of Agriculture to enact phytosanitary regulation was provided which slowed the spread of the disease and saved Washington growers millions of dollars.
2. Root pathogens of wheat can grow under extremely dry conditions. Scientists studying climate change are interested in the future distribution of wheat pathogens and pests under scenarios in the year 2050, but little is known about how root pathogens respond to temperature and moisture. ARS scientists at Pullman, Washington, with collaborators at Washington State University, conducted a series of lab and microcosm experiments with Fusarium species (spp.) that cause crown rot of wheat and Rhizoctonia spp. that cause root rot of wheat. They showed that sensitivity to moisture varies with temperature. Fusarium species were capable of growing and germinating under very dry conditions from as low as minus 7 Megapascal (MPa), but Rhizoctonia spp. did not grow much below minus 2 MPa. This information is important for growers to determine future risk of these diseases, and explains why Fusarium crown rot is exacerbated under drought conditions.
3. Root phenotyping for disease resistance. Resistance in wheat and barley to soilborne root rot pathogens has been elusive, and screening for disease resistance has been slow and time-consuming. Using 17 resistant and 17 susceptible wheat plants representing three distinct types of resistance, ARS researchers at Pullman, Washington, observed that resistance to Rhizoctonia root rot is negatively correlated to early root growth. This discovery suggests that early root growth might be a predictor of disease resistance. It will enable rapid identification of candidate resistant plants, and will shorten the screening interval up to five-fold.
4. Molecular communication in the wheat rhizosphere. Plant roots secrete exudates that sustain and mediate communication with their rhizosphere microbiome, but the biochemical basis of these processes in cereals is poorly understood. ARS scientists in Pullman, Washington, with collaborators at Washington State University, developed analytical techniques to identify compatible solutes in exudates of the model cereal plant Brachypodium distachyon. These compounds, and the technology developed to produce and analyze them, are important for studying host-microbiome interactions. They can help to explain the persistence of populations of disease-suppressive rhizobacteria on the roots of wheat grown in arid soils throughout the Pacific Northwest.
5. Dynamics of phenazine-1-carboxylic acid (PCA) in the wheat rhizosphere. PCA produced by biocontrol bacteria has a key role in the suppression of soilborne fungal root pathogens, but the basis for its persistence in the rhizosphere of dryland wheat throughout the growing season is unexplained. ARS scientists in Pullman, Washington, with collaborators at Washington State University, determined that PCA is synthesized mainly early in the season, when the soil is still moist, but that biosynthesis can continue even as soils dry and become arid. Furthermore, persistence cannot be explained by failure to undergo degradation in arid soils. These findings are important because PCA produced in the rhizosphere can suppress Rhizoctonia solani, an important pathogen of dryland wheat.
6. Phenazine-1-carboxylic acid (PCA) influences biofilm development and turnover of rhizobacterial biomass in a soil moisture-dependent manner. Bioactive compounds produced in the rhizosphere profoundly influence plant health and development, but their impact on soil nutrient dynamics and organic matter is poorly understood due to spatial and biochemical heterogeneity. ARS scientists in Pullman, Washington, with collaborators at Washington State University and Pacific Northwest National Laboratory, imaged wheat roots grown in soil mesocosms inoculated with derivatives of the PCA-producing rhizobacterium. PCA exerted moisture-dependent effects on biofilm development and the turnover of nutrients and organic matter derived from rhizobacterial biomass. These results are important because they show that key taxa within the phytobiome significantly impact rhizosphere function.
Review Publications
Thompson, A.L., Mahoney, A.K., Smiley, R.W., Paulitz, T.C., Hulbert, S., Garland Campbell, K.A. 2017. Resistance to multiple soil-borne pathogens of the Pacific Northwest is co-located in a wheat recombinant inbred line population. G3, Genes/Genomes/Genetics. 7:1109-1116.
Jaaffar, K.M., Parejko, J.A., Paulitz, T.C., Weller, D.M., Thomashow, L.S. 2017. Sensitivity of Rhizoctonia isolates from the Inland Pacific Northwest of the United States to phenazine-1-carboxylic acid and biological control by phenazine-producing Pseudomonas spp. Phytopathology. 107(6):692-703.
